Ch 10 - From DNA to Proteins: Transcription and RNA Processing
If a gene were 60 nucleotides long, where in the transcription unit would a mutation most likely affect whether or not the resulting protein was functional? -61 -35 +35 +1
-35 This nucleotide is upstream from the start site, so it is more likely to be affected by function mutations.
Which of the choices are critical elements of a bacterial promoter? Poly A Inverted repeat Inverted repeat and -35 consensus sequence -35 consensus sequence -35 consensus sequence and poly A
-35 consensus sequence
Sheila is experimenting with possible gene dysfunction based on its sequencing in bacterial cells. In her experiment, she creates a transcription marker that signals for an addition of five nucleotides to the RNA strand. The marker only activates when a guanine is paired with uracil. Assuming the probability of guanine pairing with uracil is 10%, what would be the total nucleotide count of the RNA molecule? Assume that the initial strand is 100 nucleotides long and that the base composition of g
110 nucleotides This is the correct nucleotide count of the strand. From the base composition, you can determine that there are 20 guanine nucleotides. From there, you can determine that at 10%, guanine would pair twice. Those two pairings would translate into adding 10 nucleotides to the RNA strand.
At least _ genes are involved in silencing genes using RNA interference.
2
In RNA molecules, uracil has the capacity to bind to guanine. Assuming the probability of that pairing was 10%, what would the base composition of uracil be in an RNA strand encoded from the DNA sequence shown? 5'-ACGTGGCCTAGGGGGGTAGT-3' 25% 20% 15% 50%
20% This is the correct base composition based on the combination of binding to adenine and probability of guanine binding to uracil in RNA. The total base composition is needed to find how it changes when taking probability into consideration.
An RNA molecule has the percentages of bases shown: A = 30%, U = 23%, C = 20%, and G = 27%. What is the percentage of A in the template strand of DNA that encodes this RNA, assuming that the template strand contains no introns? 27% 20% 30% 23%
23% The percentage of A in the template would be 23% because A is complementary to U.
If a theoretical organism has a total of 25 different amino acids found in its proteins, how many different tRNAs would this organism need to possess? 20 28 50 25
25 There must be a tRNA for each individual amino acid.
Polyadenylation occurs
3' of the 3' consensus sequence
If the sequence of an RNA molecule is 5'-GGCAUCGACG-3', what is the sequence of the template strand of DNA? 3'-GGCATCGACG-5' 5'-GGCATCGACG-3' 5'-CCGTAGCTGC-3' 3'-CCGTAGCTGC-5'
3'-CCGTAGCTGC-5' This sequence is both complementary and antiparallel to the product of transcription.
Antonio is creating a presentation for research on transcription using a DNA strand sample and 3-D RNA models. In order to better explain the complexities of RNA structure and base composition, he creates a model with four RNA complements. Which of these models does not abide according to what is known about RNA and base pairing? 5'-GGGCCTATTAACCAGG-3' —- 3'-CCCGGAUAAUUGGUCC-5' 5'-UCUGGUUAAUAGGUUU-3' 5'-CCUGGUUAAUAGGCCC-3' 5'-CCUAACCAAUAGGCCC-3'
5'-CCUAACCAAUAGGCCC-3' There are a couple of base pairs that would pair in this sequence, so this complement would not bind properly.
What is the important reason for understanding and applying CRISPR as a molecular technique?
A potential application of CRISPR is targeted genome editing for gene therapy.
What does a function RNA polymerase holoenzyme contain?
A sigma subunit
If a eukaryotic gene undergoes a single base pair substitution in the middle of an exon, what effect would you expect on the transcript of that gene?
A single base pair substitution in an exon would be unlikely to affect the transcript unless it created a new splice consensus site.
What is a transcription unit?
A stretch of DNA that encodes a single RNA molecule and other sequences necessary for transcription
What effect on the transcript would you expect if a eukaryotic gene underwent a two base pair deletion at the 5' end of an intron?
A two base pair deletion at the 5' end of an intron would most likely prevent the normal spicing of this intron.
The transcription site is
After the promoter of a transcription unit
The mature, processed transcript (mRNA) consists of all of these except 3' consensus sequence All are part of the mature transcript 5' cap 5' consensus sequence Exons
All are part of the mature transcript
RNA interference is involved in which of these? immune response to viruses limiting transposons spread silencing genes after they have been transcribed all of the choices none of the choices
All of the choices
Which statement is true of RNA synthesis in bacteria? It is complementary to the template strand of DNA It occurs in a transcription bubble, and it occurs in the 5' to 3' direction All of the statements are true It occurs in a transcription bubble It occurs in the 5' to 3' direction
All of the statements are true
What effect might you expect in a eukaryotic organism in which an enzyme essential for adding the 5' cap to RNA polymerase II transcripts was nonfunctional? The organism's ribosomes would not efficiently recognize mRNA transcripts produced. All of the statements will result from nonfunctional mRNA capping. The organism would be unable to produce stable mRNA transcripts. The organism would be unable to efficiently splice RNA transcripts.
All of the statements will result from nonfunctional mRNA capping.
A mutation in RNA polymerase III would likely result in which of these consequences? The cell would no longer be regulated in its gene expression. There would remain an abundance of RNA components in the nucleus. Amino acids will fail to attach during the elongation phase of transcription. The creation and functioning of ribosomes will be disrupted.
Amino acids will fail to attach during the elongation phase of transcription. This is a dysfunction from a lack in tRNA function. Transfer RNAs are typically encoded by RNA polymerase III.
Which statement is true of splicing?
Exons are spliced to exons, and the 5' end of the intron is attached to the branch point.
If the promoter that best matches the consensus sequence shown serves as the strongest promoter, then which sequence would serve as the strongest promoter? G C Y A T R N A G G T A T C T A G C C A T A A A G C A A T A G A G C G A T T C G
G C C A T A A A
Ten sequences from the upstream region of a group of genes are shown. What is the best expression of the consensus sequence derived from these actual sequences? [The illustration shows 4 actual sequences and a consensus sequence. The first actual sequence, at the top, from 5 prime to 3 prime is as follows: A, C, G, A , G, A, A, T. The second actual sequence below from 5 prime to 3 prime is as follows: G, A, C, T, A, C, T, C. The third actual sequence below from 5 prime to 3 prime is as follow
G N C T R C A Y No particular base or kind of base is more common than the others at position 2, A and G (R) are equally common at 5, and C and T (Y) are equally common at 8.
The initiation process of bacterial transcription is shown. What is the correct order of the steps? I. The holoenzyme binds the promoter and unwinds double-stranded DNA. II. rNTP complementary to the base serves as the first nucleotide in an RNA molecule. III. Sigma factor associates with core enzyme to form a holoenzyme. IV. Sigma factor is released. V. Phosphate groups are cleaved and the RNA nucleotide is added. VI. The holoenzyme binds to the -35 and -10 consensus sequences. III,
III, VI, I, II, V, IV This is the sequential order for bacterial transcription.
If the 3' consensus sequence were mutated in a particular gene, what effect would you expect on the RNA transcript?
If the 3' consensus sequence were mutated, the transcript would not be polyadenylated and would be unstable
What does a transcription unit contain?
RNA coding region, terminator, and promoter
Which of these sequences exhibit full consensus based on the nucleotide set shown? A G G A G T T C A G C T A T T C T G C A A T A C T C G A A A A G T C C T A A T G T G C A A T T C - T G C A A T T C - T C G A A T T G - A C G T G A A C - T G C A A A A G
T G C A A T T C This consensus sequence matches at all eight positions.
Why would a newly synthesized RNA molecule have three phosphate groups at its 5' end? There was a mutation in the terminator sequence, which did not allow for the removal of the phosphates. A modified ribonucleoside triphosphate was incorporated that contained three phosphate groups at its 5' end instead of its 3' end. The 5' end of the first ribonucleoside triphosphate that is incorporated is not involved in the formation of a phosphodiester bond. The phosphate groups were not removed when
The 5' end of the first ribonucleoside triphosphate that is incorporated is not involved in the formation of a phosphodiester bond. Ribonucleoside triphosphates have three phosphate groups at their 5' ends, and two of these are removed during the formation of a phosphodiester bond. The 5' end of the first ribonucleoside triphosphate is not involved in a phosphodiester bond.
Which of these best describes the first step of intron removal during mRNA processing?
The 5' end of the intron is cleaved from the preceding exon and simultaneously joined to the branch point within the intron.
Which step in mRNA processing occurs first?
The 5' end of the primary transcript is capped.
Which of these statements is true about gene structure? Every codon in the eukaryotic gene encodes an amino acid. There is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein. The number of nucleotides in a gene is always proportional to the number of amino acids in the protein encoded by that gene. The DNA can be much longer than that of mRNA originated from the gene.
The DNA can be much longer than that of mRNA originated from the gene. The DNA is clearly much longer than the mRNA because regions of DNA looped out from the hybridized molecules.
Which of these events is NOT required in order to induce termination of the transcription process? The RNA molecule partially dissociates from the DNA molecule. The newly made RNA molecule must be released from the polymerase. The RNA polymerase must detach from the DNA template. RNA polymerase halts synthesis RNA after the terminator sequence is transcribed.
The RNA molecule partially dissociates from the DNA molecule. The RNA molecule must fully dissociate from the DNA molecule before it can be incorporated into the process of translation.
Which of these events is NOT required in order to induce termination of the transcription process? The RNA polymerase must detach from the DNA template. RNA polymerase halts synthesis RNA after the terminator sequence is transcribed. The newly made RNA molecule must be released from the polymerase. The RNA molecule partially dissociates from the DNA molecule.
The RNA molecule partially dissociates from the DNA molecule. The RNA molecule must fully dissociate from the DNA molecule before it can be incorporated into the process of translation.
How is the poly (A) tail formed? The addition of a methyl group to the 1 position of adenine. The addition of a methyl group to nitrogen at the 6 position of adenine. The addition of an extra guanine nucleotide to the 5' end of the mRNA and the addition of methyl groups to the base in that guanine. The addition of 50 to 250 or more adenine nucleotides at the 3' end.
The addition of 50 to 250 or more adenine nucleotides at the 3' end. A type of modification to eukaryotic mRNA is the addition of 50 to 250 or more adenine nucleotides at the 3' end, forming a poly (A) tail.
David is assessing the frequencies of base sequences in DNA and RNA. He wants to determine the differences in stability between an RNA complement of a DNA strand and a model RNA isolated from a different culture earlier. The DNA and model RNA strands are shown. Which conclusion can David deduce from comparing the RNA strands? DNA strand: 5'-GGCCATATGCTAGCTTAAGC-3' Model RNA: 5'-AGGUUCCAUGGACCUUAACG-3' The base composition of both the RNA complement and the model RNA are the same. The model R
The base composition of both the RNA complement and the model RNA are the same. Both strands share the same composition with each base being expressed at 25%.
A mutation in RNA polymerase II would likely result in which of these consequences? The cell would no longer be regulated in its gene expression. There would remain an abundance of RNA components in the nucleus. The creation and functioning of ribosomes will be disrupted. Amino acids will fail to attach during the elongation phase of transcription.
The cell would no longer be regulated in its gene expression. Gene expression in a cell is mediated by miRNAs. MicroRNA and siRNAs are limiters that restrict the cell in its action during transcription. An overexpression of genes could be a result of a dysfunction in either one of these products.
Which of these statements is FALSE regarding promoter significance in prompting functionality during initiation? The duration of binding has no effect on the affinity of promoters in relation to RNA polymerases. The introduction of consensus sequences with a high affinity for various promoters dictates a high degree of significant function. The location of the consensus sequence in relation to the promoter can determine the rate of initiation and the likelihood of point mutations taking place
The duration of binding has no effect on the affinity of promoters in relation to RNA polymerases. Promoters are sensitive to time, and based on that time, the effect of the promoter's affinity toward RNA polymerase varies from one type to the next.
Which of these statements concerning bacterial RNA polymerase is FALSE? The omega subunit is not essential for transcription or enzyme stability. The alpha and beta units primarily function in the catalysis of RNA elongation through nucleotide addition. The formation of the holoenzyme is dependent on associative binding of sigma factor. Without sigma factor, RNA polymerase will initiate transcription at a primary point along DNA.
The omega subunit is not essential for transcription or enzyme stability. The omega subunit is used for stabilizing the core enzyme used in transcription.
If you are performing an in vitro transcription experiment in the bacterium E. coli and you keep transcribing random mRNAs of varying lengths, what might be your issue? The sigma factor is not binding to the core enzyme. The core enzyme is not functioning. The sigma factor is not dissociating from the holoenzyme. The holoenzyme is not binding to its substrate.
The sigma factor is not binding to the core enzyme. The sigma factor controls the binding of RNA polymerase to the promoter, so the dysfunction can be related to the function of sigma factor.
What role do CRISPR-Cas systems naturally play in bacteria? They defend prokaryotic cells against invasion by foreign DNA. They combine with Piwi proteins. They are transcribed from enhancer sequences. They are cleaved by the enzyme Dicer.
They defend prokaryotic cells against invasion by foreign DNA. In acquisition, foreign DNA from a bacteriophage or plasmid that enters the cell is identified, processed, and inserted into the CRISPR array as a new spacer between the palindromic repeats.
If pre-mRNA processing fails, which of these can result?
Translation may not occur
Inverted repeats in _ cause(s) the formation of hairpin loops.
a microRNA sequence
If Gene A is transcribed from the top strand of DNA and Gene B is transcribed from the bottom strand of DNA, then the coding sequence for Gene A is located on the top strand of DNA only. the template strand only. the bottom strand of DNA only. both strands of DNA.
both strands of DNA. DNA runs both strands antiparallel from one another, so the sequence would be seen on both ends of DNA.
What transcription unit elements are included in the RNA-coding region? both the transcription start site and the terminator promoter terminator only transcription start site only
both the transcription start site and the terminator The RNA-coding region contains the start site and the terminator sequence.
The process of intron splicing involves which of these?
branch point
How does RNA interference reduce the amount of gene product produced from an mRNA?
by the binding of single-stranded microRNAs to a near complement in a target mRNA
What causes the release of RNA polymerase from the consensus sequences in the promoter? the sigma factor the unwinding of the DNA template strand the dissociation of the promoter from the transcription unit conformational change of the RNA polymerase itself
conformational change of the RNA polymerase itself The conformation change absolves the binding of the RNA from the consensus sequences in the promoter and allows it to proceed down the strand.
Which of these best describes the consensus site required for splicing introns during mRNA processing?
consensus sequences at the 5' and 3' splice sites as well as a branch point consensus sequence within the intron
In bacteria, the core enzyme of the RNA polymerase is made up of five subunits. sigma factor. RNA. holoenzyme.
five subunits. The core enzyme is composed of two copies of the alpha subunit, and single copies of the beta, beta prime, and omega subunits.
DNA from a eukaryotic gene was isolated, denatured, and hybridized to the mRNA transcribed from the gene. The hybridized structure was then observed with an electron microscope. The image is shown. Based on these results, the gene must contain _____ exons and _____ introns. [A line drawing represents the structure of DNA hybridized to m RNA. The drawing shows a wavy line with 3 loops above the line and 2 loops below it.] four; five four; four five; four five; five
five; four There are four introns indicated by the four loops, and the number of exons is one more than the number of introns.
What is the source of the unique sequences found in CRISPR?
foreign invading DNA
What is the primary role of CRISPR?
generating adaptive immune system against foreign invaders
Which of these is not part of the eukaryotic RNA processing?
initiation
The stages of bacterial transcription, listed in the correct order, are initiation, elongation, and termination. unwinding, elongation, and termination. unwinding, promotion, elongation, and termination. promotion, elongation, and termination.
initiation, elongation, and termination. This is the correct sequence of bacterial transcription.
Which of these is involved in RNA interference? snoRNA snRNA tRNA miRNA
miRNA miRNA molecules are generally not derived from their target genes and do not inhibit transcription.
Which of these types of genes would typically contain only nucleotide sequences designed for amino acid sequence of a protein? both bacterial and eukaryotic genes a typical eukaryotic gene a typical bacterial gene neither bacterial nor eukaryotic genes
neither bacterial nor eukaryotic genes This notion does not account for sequences that are transcribed but are not part of the coding region in both bacterial and eukaryotic genes.
What is the key function of CRISPR-associated proteins or CAS?
nuclease
CRISPR consists of a series of _ sequences that read the same forward and backward on two complementary strands, separated by unique sequences.
palindromic
Which of the choices are critical elements of a bacterial terminator? Poly A -10 consensus sequence and poly A Inverted repeat Poly A and inverted repeat -10 consensus sequence
poly A and inverted repeat
Which type of RNA molecule is found in eukaryotes but not bacteria? mRNA rRNA tRNA pre-mRNA
pre-mRNA The primary products of transcription in eukaryotic cells are large precursor molecules called pre-mRNA that are modified extensively before becoming mRNA.
Which of these types of RNA becomes structural and functional components of the ribosome subunits? mRNA tRNA rRNA pre-mRNA
rRNA Ribosomal RNA (rRNA) and ribosomal protein subunits make up the ribosome, the site of protein assembly.
Which type of RNA molecule can accomplish RNA interference by inhibiting transcription and generally is derived from sequences within the genes that it regulates? miRNA siRNA snoRNA piRNA
siRNA siRNA molecules are derived from their target genes and can inhibit transcription of target genes.
When a(n) _ in RISC binds to a target mRNA, there is no gene product, but when a(n) _ in RISC binds to a target mRNA, there is less gene product than normal
siRNA and microRNA
How is siRNA different than miRNA? siRNA molecules inhibit transcription. siRNA molecules target genes from which they were not transcribed. siRNA molecules are longer. siRNA molecules degrade mRNA.
siRNA molecules inhibit transcription. miRNAs often suppress gene expression by inhibiting translation.
Which of these is not involved in gene silencing using RNA interference? Target gene Dicer Hairpin loop Splicer RISC
splicer
Selene is targeting RNA molecules for a function test. She introduces a molecule that signals a cascade that causes the lysosome to degrade the nucleus. Which of these molecules would not be immediately affected by the action of the lysosome? tRNA mRNA pre-mRNA snRNA
tRNA Transfer RNA are primarily housed in the cytoplasm and would not be readily affected by the action of the lysosome.
The structure of tRNA described as L-shaped is the _____ structure. secondary tertiary quaternary primary
tertiary The cloverleaf folds on itself to form an L-shaped structure, with the acceptor stem at one end of the tertiary structure and the anticodon at the other end.
How are miRNAs and siRNAs similar? Both interact with and use Dicer and RISC. Both have perfect base pairing to the mRNA target. Both form hairpins. Both begin as double-stranded RNA.
th interact with and use Dicer and RISC. Both siRNA and miRNA molecules combine with proteins to form an RNA-induced silencing complex (RISC).
What causes the formation of an RNA hairpin?
the inverted repeat of the terminator
In what location(s) are all eukaryotic RNAs synthesized? the nucleus only the cytoplasm only the cell membrane only the nucleus and cytoplasm
the nucleus only All eukaryotic RNAs are synthesized in the nucleus, even though they may function in other areas.
Which process in eukaryotes is shown in the electron micrograph? [Under the electron microscope, DNA molecules undergoing transcription exhibit Christmas-tree-like structures. This is an image of an electron micrograph of transcription units.] replication transcription translation RNA processing
transcription The strands that connect the "Christmas trees" (trunks) are DNA molecules, and the strands extending from the DNA molecules (branches) are RNAs of different lengths, depending on how much of each gene has been transcribed.
